The head of US Central Command urged greater trust and communications with the Pakistani military on Monday amid a diplomatic crisis after US air strikes killed 24 Pakistani soldiers last month.

General James Mattis made his recommendations after his command, which oversees US military operations across a wide swath of North Africa, the Middle East and Central Asia, released the results of its own investigation into the November 25-26 incident.

A joint US-NATO investigation unveiled last week portrayed a disastrous spate of errors and botched communication in which both sides failed to inform the other about their operational plans or the location of troops.

"The strongest take-away from this incident is the fundamental fact that we must improve border coordination and this requires a foundational level of trust on both sides of the border," Mattis said in a statement.

The deadliest single cross-border attack of the 10-year war in Afghanistan, the strike has plunged the precarious Pakistani-US alliance to its lowest ebb in a decade with both sides in dispute about the precise sequence of events.

Islamabad rejected the earlier US inquiry after the Americans insisted their troops responded only after coming under heavy machine-gun and mortar fire.

It also refused to take part in the probe and instead sought a formal apology from US President Barack Obama, dissatisfied with condolences and expressions of regret from the Americans.

Although the US-NATO probe acknowledged the Americans had relayed "incorrect mapping information" to a Pakistani liaison officer that gave the wrong location for Pakistani troops at border outposts, the CENTCOM report made no mention of discipline of US or NATO personnel.

But Mattis directed NATO's International Security Assistance Force (ISAF) commander General John Allen to take a number of corrective actions to improve the now-moribund relationship with Islamabad, including fostering "improved, mutual trust" between forces working in the mostly lawless border areas.

Troops should also "clarify authorities, responsibilities, and standard operating procedures" in the area as well as conduct formal exercises and drills to improve coordination and reduce chances of conflict.

Mattis also called for "full disclosure of all border area facilities and installations" on both sides of the border, with updates using a shared database and map as well as organizing coordination visits.

His comments came as The New York Times reported that the United States is bracing for a limited counterterrorism alliance with Pakistan, as a deterioration in ties complicates the ability to launch attacks against extremists and move supplies into Afghanistan.

"We've closed the chapter on the post-9/11 period," the Times quoted a senior US official as saying. "Pakistan has told us very clearly that they are re-evaluating the entire relationship."

The shift means the United States will be forced to restrict drone strikes, limit the number of its spies and soldiers on the ground and spend more to transport supplies through Pakistan to allied troops in Afghanistan, according to the report. It said US said to Pakistan would also drop sharply.

A Los Angeles Times report over the weekend said the CIA has already suspended drone missile strikes on gatherings of low-ranking militants in Pakistan due to tensions with Islamabad.